The recent growing interest in the biological properties of lichen metabolites has evidenced different needs and challenges for further exploration, including the development of green processing with safer solvents and more efficient use of energy. Microwave assisted hydrothermal processing, applied after supercritical CO2 extraction, was proposed for the sequential extraction of bioactives and biopolymer fractions. Alternatively, it was combined with natural deep eutectics (NaDES) as cosolvents. Lichenic acids, antioxidants and oligosaccharides were simultaneously extracted using NaDES, and the recovered polysaccharides showed adequate mechanical properties for the formulation of films with antimicrobial action against Gram positive bacteria. An environmental assessment of the three different processes using the Eco-Scale suggested that the NaDES microwave extraction was, due to its low toxicity and good extraction yield of polysaccharides, the most sustainable of the three processes.